Multiple sequence alignment - TraesCS7B01G220300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G220300 chr7B 100.000 4719 0 0 1 4719 411503450 411498732 0.000000e+00 8715.0
1 TraesCS7B01G220300 chr7D 93.669 2006 78 23 2718 4712 401843716 401841749 0.000000e+00 2955.0
2 TraesCS7B01G220300 chr7D 90.521 2226 152 28 197 2380 401847449 401845241 0.000000e+00 2887.0
3 TraesCS7B01G220300 chr7D 92.531 723 38 6 1719 2429 401844929 401844211 0.000000e+00 1022.0
4 TraesCS7B01G220300 chr7D 93.162 234 11 3 2469 2699 401843934 401843703 5.850000e-89 339.0
5 TraesCS7B01G220300 chr7D 92.896 183 12 1 1 182 401848609 401848427 1.010000e-66 265.0
6 TraesCS7B01G220300 chr7A 90.931 2040 112 37 2718 4719 459633477 459631473 0.000000e+00 2675.0
7 TraesCS7B01G220300 chr7A 92.274 1838 69 21 913 2699 459635278 459633463 0.000000e+00 2540.0
8 TraesCS7B01G220300 chr7A 84.676 757 75 21 7 757 459636601 459635880 0.000000e+00 717.0
9 TraesCS7B01G220300 chr5B 76.355 406 63 21 356 757 711918334 711918710 2.240000e-43 187.0
10 TraesCS7B01G220300 chr5B 78.341 217 26 12 222 423 527037572 527037362 2.310000e-23 121.0
11 TraesCS7B01G220300 chr4A 75.399 439 75 18 222 652 21235725 21236138 1.040000e-41 182.0
12 TraesCS7B01G220300 chr3A 81.169 154 23 6 276 423 95367199 95367352 8.300000e-23 119.0
13 TraesCS7B01G220300 chr1A 77.093 227 34 11 222 431 499766324 499766549 1.070000e-21 115.0
14 TraesCS7B01G220300 chr1D 92.683 41 2 1 399 439 478332461 478332500 1.830000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G220300 chr7B 411498732 411503450 4718 True 8715.000000 8715 100.000000 1 4719 1 chr7B.!!$R1 4718
1 TraesCS7B01G220300 chr7D 401841749 401848609 6860 True 1493.600000 2955 92.555800 1 4712 5 chr7D.!!$R1 4711
2 TraesCS7B01G220300 chr7A 459631473 459636601 5128 True 1977.333333 2675 89.293667 7 4719 3 chr7A.!!$R1 4712

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
987 2411 0.241213 GAGCCCAACGGAAAGCTTTC 59.759 55.000 27.68 27.68 35.23 2.62 F
1046 2474 1.007849 CCTCGCAAAACCAAACCGG 60.008 57.895 0.00 0.00 42.50 5.28 F
2639 5307 0.188342 ACCCCTTGTTGCACCTCAAT 59.812 50.000 0.00 0.00 36.99 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 5307 0.110486 GTTTGCAACCCCTCTCTGGA 59.890 55.0 0.00 0.00 38.35 3.86 R
2689 5360 0.684535 TTTGCGGGTGATCTCTGTGA 59.315 50.0 0.00 0.00 0.00 3.58 R
3781 6480 0.038892 GAACTTGGGCACATGCACTG 60.039 55.0 7.77 3.11 46.62 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 5.525745 TCTGTGTTCTTTTGATGCTTCGTTA 59.474 36.000 0.00 0.00 0.00 3.18
98 100 7.814587 TCAATGAAATCAGCTCGATTCGTATAT 59.185 33.333 5.89 0.00 43.83 0.86
162 164 2.106332 GGCCTACGACATCCCACG 59.894 66.667 0.00 0.00 0.00 4.94
163 165 2.718073 GGCCTACGACATCCCACGT 61.718 63.158 0.00 0.00 44.72 4.49
165 167 1.518572 CCTACGACATCCCACGTGC 60.519 63.158 10.91 0.00 42.61 5.34
187 1158 1.663074 CTCCTATTCAGCGCGCTCC 60.663 63.158 34.28 1.18 0.00 4.70
188 1159 3.032609 CCTATTCAGCGCGCTCCG 61.033 66.667 34.28 22.12 40.75 4.63
463 1437 6.487668 TGCGAGTGAATTTGGATATTGATGAT 59.512 34.615 0.00 0.00 0.00 2.45
502 1476 9.585099 TTGATGAACATCTTTAACAATTATGGC 57.415 29.630 14.50 0.00 38.60 4.40
524 1498 5.748630 GGCGAACAAAATTTGAATAGGATCC 59.251 40.000 13.19 2.48 0.00 3.36
810 2172 7.993821 TTCGCAAAAACATGTGAAGAAATTA 57.006 28.000 0.00 0.00 42.97 1.40
930 2354 2.996621 GAGCTAAAGCACGTGATTCAGT 59.003 45.455 20.68 7.00 45.16 3.41
987 2411 0.241213 GAGCCCAACGGAAAGCTTTC 59.759 55.000 27.68 27.68 35.23 2.62
1046 2474 1.007849 CCTCGCAAAACCAAACCGG 60.008 57.895 0.00 0.00 42.50 5.28
1332 2760 2.764314 GCGCAACAGCAGGGTATGG 61.764 63.158 0.30 0.00 37.05 2.74
1391 2825 5.300286 CCTATGCCTCTTCCTTGTTTATTGG 59.700 44.000 0.00 0.00 0.00 3.16
1620 3054 4.046462 CACAAGATTGCACTTCACCTTTG 58.954 43.478 0.00 0.00 0.00 2.77
1623 3057 3.825328 AGATTGCACTTCACCTTTGACT 58.175 40.909 0.00 0.00 0.00 3.41
1640 3074 5.772393 TTGACTGTCATAACCCTAACCAT 57.228 39.130 11.86 0.00 0.00 3.55
1674 3113 6.435277 AGACAAAGGATCAATAGCAACACAAT 59.565 34.615 0.00 0.00 0.00 2.71
1686 3125 9.596677 CAATAGCAACACAATTTTGTAAATTGG 57.403 29.630 21.95 15.45 39.91 3.16
1716 3155 3.979101 AATAAACAGCCCCACAATTGG 57.021 42.857 10.83 0.00 43.50 3.16
1739 3178 6.070251 TGGCAACTCTTGGTTTCTCTCATATA 60.070 38.462 0.00 0.00 35.74 0.86
1869 3310 2.092429 GGAAGGCCATGTCCAAGTATCA 60.092 50.000 5.01 0.00 33.79 2.15
1881 4302 3.388024 TCCAAGTATCATCTACCCTGCAC 59.612 47.826 0.00 0.00 0.00 4.57
1940 4361 7.956328 ACTTGTTCATCATAGTAGTCCTACA 57.044 36.000 7.19 0.00 38.48 2.74
2030 4455 2.902608 AGTGTCAAGTAGGGATCACCA 58.097 47.619 0.00 0.00 43.89 4.17
2051 4476 1.485480 TGGGTTGACGGACTTAACACA 59.515 47.619 0.00 0.00 35.53 3.72
2088 4513 4.764172 CTCTCGATCCCAAATGAGAACTT 58.236 43.478 0.00 0.00 37.06 2.66
2162 4587 4.722700 GGTGGCACCATGACCGCT 62.723 66.667 31.26 0.00 38.42 5.52
2233 4658 5.221126 GCCTTTGATTCTTTGTCAGACAACT 60.221 40.000 15.93 1.32 37.90 3.16
2274 4699 1.616327 CTGGTGGATGGAGGGGTCA 60.616 63.158 0.00 0.00 0.00 4.02
2310 4735 1.150536 GGTGTTGGTGGGAGCTGAA 59.849 57.895 0.00 0.00 0.00 3.02
2446 4897 5.277106 GCCAACCTTTTCCATTTGTTTTACG 60.277 40.000 0.00 0.00 0.00 3.18
2517 5185 3.670627 GCCTCTAAAAATTGGCGTGAGTG 60.671 47.826 0.00 0.00 35.79 3.51
2579 5247 2.363276 TACCATGGCCGTCGACCT 60.363 61.111 13.04 0.00 0.00 3.85
2596 5264 3.181480 CGACCTGGAATTGTTTGGTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
2639 5307 0.188342 ACCCCTTGTTGCACCTCAAT 59.812 50.000 0.00 0.00 36.99 2.57
2685 5356 5.409520 GCGATCCTGATATTGTGCATAAGAA 59.590 40.000 1.43 0.00 0.00 2.52
2686 5357 6.619446 GCGATCCTGATATTGTGCATAAGAAC 60.619 42.308 1.43 0.00 0.00 3.01
2687 5358 6.648310 CGATCCTGATATTGTGCATAAGAACT 59.352 38.462 1.43 0.00 0.00 3.01
2688 5359 7.814587 CGATCCTGATATTGTGCATAAGAACTA 59.185 37.037 1.43 0.00 0.00 2.24
2689 5360 9.664332 GATCCTGATATTGTGCATAAGAACTAT 57.336 33.333 1.43 0.00 0.00 2.12
2690 5361 9.664332 ATCCTGATATTGTGCATAAGAACTATC 57.336 33.333 1.43 5.04 0.00 2.08
2691 5362 8.650490 TCCTGATATTGTGCATAAGAACTATCA 58.350 33.333 13.35 13.35 0.00 2.15
2692 5363 8.715998 CCTGATATTGTGCATAAGAACTATCAC 58.284 37.037 11.14 0.00 0.00 3.06
2693 5364 9.264719 CTGATATTGTGCATAAGAACTATCACA 57.735 33.333 11.14 0.00 31.67 3.58
2694 5365 9.264719 TGATATTGTGCATAAGAACTATCACAG 57.735 33.333 11.14 0.00 33.47 3.66
2695 5366 9.481340 GATATTGTGCATAAGAACTATCACAGA 57.519 33.333 1.43 0.00 33.47 3.41
2696 5367 7.783090 ATTGTGCATAAGAACTATCACAGAG 57.217 36.000 1.43 0.00 33.47 3.35
2697 5368 6.530019 TGTGCATAAGAACTATCACAGAGA 57.470 37.500 0.00 0.00 30.82 3.10
2698 5369 7.117285 TGTGCATAAGAACTATCACAGAGAT 57.883 36.000 0.00 0.00 40.86 2.75
2699 5370 7.205992 TGTGCATAAGAACTATCACAGAGATC 58.794 38.462 0.00 0.00 38.19 2.75
2700 5371 7.147846 TGTGCATAAGAACTATCACAGAGATCA 60.148 37.037 0.00 0.00 38.19 2.92
2701 5372 7.168972 GTGCATAAGAACTATCACAGAGATCAC 59.831 40.741 0.00 0.00 38.19 3.06
2702 5373 6.644592 GCATAAGAACTATCACAGAGATCACC 59.355 42.308 0.00 0.00 38.19 4.02
2703 5374 5.606348 AAGAACTATCACAGAGATCACCC 57.394 43.478 0.00 0.00 38.19 4.61
2704 5375 3.634448 AGAACTATCACAGAGATCACCCG 59.366 47.826 0.00 0.00 38.19 5.28
2705 5376 1.683917 ACTATCACAGAGATCACCCGC 59.316 52.381 0.00 0.00 38.19 6.13
2706 5377 1.683385 CTATCACAGAGATCACCCGCA 59.317 52.381 0.00 0.00 38.19 5.69
2707 5378 0.904649 ATCACAGAGATCACCCGCAA 59.095 50.000 0.00 0.00 28.20 4.85
2708 5379 0.684535 TCACAGAGATCACCCGCAAA 59.315 50.000 0.00 0.00 0.00 3.68
2709 5380 1.071542 TCACAGAGATCACCCGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
2710 5381 1.879380 CACAGAGATCACCCGCAAAAA 59.121 47.619 0.00 0.00 0.00 1.94
2825 5499 6.549364 TGTGGTCCTAATGTTTCATTCACTTT 59.451 34.615 0.00 0.00 0.00 2.66
2872 5546 6.098679 CGAATAAGCAAATCAACAAATCCCA 58.901 36.000 0.00 0.00 0.00 4.37
2905 5579 7.550712 AGGATAACTGATTTTGAAATGAAGGC 58.449 34.615 0.00 0.00 0.00 4.35
2918 5592 7.377766 TGAAATGAAGGCATCTTGTACTTAC 57.622 36.000 0.00 0.00 32.35 2.34
2947 5621 6.038825 TGTTCGTTGTTGGTTAATTGTCTGAT 59.961 34.615 0.00 0.00 0.00 2.90
2995 5669 1.337823 CGGAGAGTTTTCACGGTGGAT 60.338 52.381 8.50 0.00 0.00 3.41
3188 5866 8.732746 TTAGCATTTCCTCCTAGTGAATAAAC 57.267 34.615 0.00 0.00 0.00 2.01
3227 5917 8.408601 GTTATTGATTTCAAGCCACTACATCAT 58.591 33.333 0.00 0.00 39.47 2.45
3228 5918 6.441093 TTGATTTCAAGCCACTACATCATC 57.559 37.500 0.00 0.00 0.00 2.92
3229 5919 5.748402 TGATTTCAAGCCACTACATCATCT 58.252 37.500 0.00 0.00 0.00 2.90
3230 5920 6.888105 TGATTTCAAGCCACTACATCATCTA 58.112 36.000 0.00 0.00 0.00 1.98
3231 5921 7.512130 TGATTTCAAGCCACTACATCATCTAT 58.488 34.615 0.00 0.00 0.00 1.98
3232 5922 7.994911 TGATTTCAAGCCACTACATCATCTATT 59.005 33.333 0.00 0.00 0.00 1.73
3233 5923 9.494271 GATTTCAAGCCACTACATCATCTATTA 57.506 33.333 0.00 0.00 0.00 0.98
3304 5999 9.214953 CTAAATAACATTCTTCTCAAATGCGTC 57.785 33.333 0.00 0.00 37.58 5.19
3306 6001 3.067106 ACATTCTTCTCAAATGCGTCGT 58.933 40.909 0.00 0.00 37.58 4.34
3314 6009 0.858583 CAAATGCGTCGTGTCACTGA 59.141 50.000 0.65 0.00 0.00 3.41
3319 6014 0.179161 GCGTCGTGTCACTGATAGCT 60.179 55.000 0.65 0.00 0.00 3.32
3324 6019 2.359214 TCGTGTCACTGATAGCTGATCC 59.641 50.000 0.00 0.00 33.07 3.36
3325 6020 2.736978 GTGTCACTGATAGCTGATCCG 58.263 52.381 0.00 0.00 33.07 4.18
3330 6025 4.920340 GTCACTGATAGCTGATCCGTATTG 59.080 45.833 0.00 0.00 31.38 1.90
3580 6279 0.520404 CAAGTTGCTGTGCTAGGCTG 59.480 55.000 0.00 0.00 0.00 4.85
3591 6290 0.397254 GCTAGGCTGTGGAGGACCTA 60.397 60.000 0.00 0.00 37.04 3.08
3629 6328 1.202891 GGGTGTGGTCTGGCTAGTTTT 60.203 52.381 0.00 0.00 0.00 2.43
3650 6349 8.135529 AGTTTTCAGGACTTGTTTATGCTTTAC 58.864 33.333 0.00 0.00 0.00 2.01
3741 6440 4.071961 TGCAGAGCTTTGTACTCAGAAA 57.928 40.909 6.08 0.00 36.58 2.52
3742 6441 4.450976 TGCAGAGCTTTGTACTCAGAAAA 58.549 39.130 6.08 0.00 36.58 2.29
3746 6445 4.985409 AGAGCTTTGTACTCAGAAAAGTCG 59.015 41.667 0.00 0.00 36.58 4.18
3758 6457 5.691815 TCAGAAAAGTCGTTTGTTTTCGTT 58.308 33.333 0.00 0.00 44.12 3.85
3767 6466 8.450385 AGTCGTTTGTTTTCGTTTAAATTTGA 57.550 26.923 0.00 0.00 0.00 2.69
3787 6486 9.598517 AATTTGAAAAGATAAAAAGTCAGTGCA 57.401 25.926 0.00 0.00 0.00 4.57
3797 6496 0.892358 AGTCAGTGCATGTGCCCAAG 60.892 55.000 2.07 0.00 41.18 3.61
3809 6508 3.515562 TGTGCCCAAGTTCCCATATTTT 58.484 40.909 0.00 0.00 0.00 1.82
3810 6509 3.260380 TGTGCCCAAGTTCCCATATTTTG 59.740 43.478 0.00 0.00 0.00 2.44
3811 6510 3.513515 GTGCCCAAGTTCCCATATTTTGA 59.486 43.478 0.00 0.00 0.00 2.69
3814 6513 4.935205 GCCCAAGTTCCCATATTTTGAAAC 59.065 41.667 0.00 0.00 0.00 2.78
3817 6517 5.639082 CCAAGTTCCCATATTTTGAAACAGC 59.361 40.000 0.00 0.00 0.00 4.40
3824 6524 5.754890 CCCATATTTTGAAACAGCTTATGGC 59.245 40.000 9.03 0.00 35.40 4.40
3863 6563 5.029807 TGTTTGCATCCATATCCTCGTTA 57.970 39.130 0.00 0.00 0.00 3.18
4068 6768 5.733647 ACCATATCTTCCTCCTTTTTCCTCT 59.266 40.000 0.00 0.00 0.00 3.69
4129 6829 0.548510 GACCAGCAAGGCTCCCTAAT 59.451 55.000 0.00 0.00 43.14 1.73
4297 6999 2.607811 CAGGCAGTGGTCCTGGATA 58.392 57.895 0.00 0.00 45.62 2.59
4300 7002 1.291033 AGGCAGTGGTCCTGGATAGTA 59.709 52.381 0.00 0.00 41.81 1.82
4301 7003 1.689273 GGCAGTGGTCCTGGATAGTAG 59.311 57.143 0.00 0.00 41.81 2.57
4321 7023 0.767375 TTTGCTCTCCTCTGCCTTGT 59.233 50.000 0.00 0.00 0.00 3.16
4479 7188 6.189859 AGGAGAGAAAATTCAATGCACCATA 58.810 36.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.880027 GCCCACACCTGTGTCTAAAAG 59.120 52.381 0.00 0.00 42.83 2.27
33 34 6.494842 TCAAAAGAACACAGACACAATAAGC 58.505 36.000 0.00 0.00 0.00 3.09
37 38 5.068198 AGCATCAAAAGAACACAGACACAAT 59.932 36.000 0.00 0.00 0.00 2.71
67 68 4.763073 TCGAGCTGATTTCATTGACTCAT 58.237 39.130 0.00 0.00 0.00 2.90
98 100 0.740149 CATTAATCAGCTTGCGGGCA 59.260 50.000 3.66 0.00 34.17 5.36
162 164 0.872021 CGCTGAATAGGAGGACGCAC 60.872 60.000 0.00 0.00 0.00 5.34
163 165 1.437573 CGCTGAATAGGAGGACGCA 59.562 57.895 0.00 0.00 0.00 5.24
165 167 1.658717 CGCGCTGAATAGGAGGACG 60.659 63.158 5.56 0.00 0.00 4.79
195 1166 4.660938 GCACTGTGACCCACCCCC 62.661 72.222 12.86 0.00 32.73 5.40
198 1169 4.927782 TGCGCACTGTGACCCACC 62.928 66.667 5.66 0.00 32.73 4.61
199 1170 3.649986 GTGCGCACTGTGACCCAC 61.650 66.667 32.55 10.54 34.56 4.61
200 1171 4.927782 GGTGCGCACTGTGACCCA 62.928 66.667 36.84 1.71 0.00 4.51
202 1173 4.626081 AGGGTGCGCACTGTGACC 62.626 66.667 36.84 28.46 0.00 4.02
203 1174 2.591715 AAGGGTGCGCACTGTGAC 60.592 61.111 36.84 21.30 0.00 3.67
204 1175 2.591429 CAAGGGTGCGCACTGTGA 60.591 61.111 36.84 0.00 0.00 3.58
348 1321 7.148306 GGCTCCACGAACTTTTTGAATCTAATA 60.148 37.037 0.00 0.00 0.00 0.98
349 1322 6.349363 GGCTCCACGAACTTTTTGAATCTAAT 60.349 38.462 0.00 0.00 0.00 1.73
350 1323 5.048991 GGCTCCACGAACTTTTTGAATCTAA 60.049 40.000 0.00 0.00 0.00 2.10
351 1324 4.454504 GGCTCCACGAACTTTTTGAATCTA 59.545 41.667 0.00 0.00 0.00 1.98
352 1325 3.253432 GGCTCCACGAACTTTTTGAATCT 59.747 43.478 0.00 0.00 0.00 2.40
353 1326 3.004315 TGGCTCCACGAACTTTTTGAATC 59.996 43.478 0.00 0.00 0.00 2.52
357 1330 2.861462 TTGGCTCCACGAACTTTTTG 57.139 45.000 0.00 0.00 0.00 2.44
358 1331 3.878160 TTTTGGCTCCACGAACTTTTT 57.122 38.095 0.00 0.00 0.00 1.94
479 1453 7.995289 TCGCCATAATTGTTAAAGATGTTCAT 58.005 30.769 0.00 0.00 0.00 2.57
493 1467 9.904647 CTATTCAAATTTTGTTCGCCATAATTG 57.095 29.630 8.89 0.00 35.64 2.32
502 1476 7.312154 TGTGGATCCTATTCAAATTTTGTTCG 58.688 34.615 14.23 0.00 0.00 3.95
930 2354 1.343465 GAGGAAGTGGACTTTCGTGGA 59.657 52.381 0.00 0.00 36.57 4.02
987 2411 1.133761 TGACGAGAGGATGAGGTAGGG 60.134 57.143 0.00 0.00 0.00 3.53
1046 2474 1.253044 CGCGTGTTGTCGTTTGCTTC 61.253 55.000 0.00 0.00 0.00 3.86
1347 2775 1.290134 GGGAGGGAAGAGATTGGTGT 58.710 55.000 0.00 0.00 0.00 4.16
1686 3125 7.327214 TGTGGGGCTGTTTATTTCATTTAATC 58.673 34.615 0.00 0.00 0.00 1.75
1691 3130 5.760484 ATTGTGGGGCTGTTTATTTCATT 57.240 34.783 0.00 0.00 0.00 2.57
1716 3155 7.849804 TTATATGAGAGAAACCAAGAGTTGC 57.150 36.000 0.00 0.00 39.19 4.17
1739 3178 6.953520 TCACCTGAATTAAGATGGAAACCATT 59.046 34.615 4.74 0.00 45.26 3.16
1809 3250 6.155827 GCTTGTCAGTGGCAAATTATTTACA 58.844 36.000 11.98 0.00 0.00 2.41
1881 4302 6.142320 GTCAAGAAAAACTGTGATAAAAGCCG 59.858 38.462 0.00 0.00 0.00 5.52
1910 4331 7.764443 GGACTACTATGATGAACAAGTTAGCAA 59.236 37.037 0.00 0.00 0.00 3.91
1940 4361 3.788142 ACCCATGATCCCTGTTTCTATGT 59.212 43.478 0.00 0.00 0.00 2.29
2030 4455 2.105134 TGTGTTAAGTCCGTCAACCCAT 59.895 45.455 0.00 0.00 0.00 4.00
2051 4476 1.322442 GAGAGCAACTGTTTTGGGCT 58.678 50.000 3.11 3.11 37.56 5.19
2160 4585 3.056313 GCGGGCAACATCCAAGAGC 62.056 63.158 0.00 0.00 39.74 4.09
2161 4586 2.409870 GGCGGGCAACATCCAAGAG 61.410 63.158 0.00 0.00 39.74 2.85
2162 4587 2.361104 GGCGGGCAACATCCAAGA 60.361 61.111 0.00 0.00 39.74 3.02
2233 4658 3.717707 GATAGATTGAAGCACCGCTGTA 58.282 45.455 0.00 0.00 39.62 2.74
2274 4699 0.617413 CCCATCCTGCTGTCACTTCT 59.383 55.000 0.00 0.00 0.00 2.85
2596 5264 1.289160 CTCTTTGGGAGGATGGGTCA 58.711 55.000 0.00 0.00 38.35 4.02
2639 5307 0.110486 GTTTGCAACCCCTCTCTGGA 59.890 55.000 0.00 0.00 38.35 3.86
2685 5356 1.683917 GCGGGTGATCTCTGTGATAGT 59.316 52.381 0.00 0.00 35.14 2.12
2686 5357 1.683385 TGCGGGTGATCTCTGTGATAG 59.317 52.381 0.00 0.00 35.14 2.08
2687 5358 1.775385 TGCGGGTGATCTCTGTGATA 58.225 50.000 0.00 0.00 35.14 2.15
2688 5359 0.904649 TTGCGGGTGATCTCTGTGAT 59.095 50.000 0.00 0.00 38.27 3.06
2689 5360 0.684535 TTTGCGGGTGATCTCTGTGA 59.315 50.000 0.00 0.00 0.00 3.58
2690 5361 1.522668 TTTTGCGGGTGATCTCTGTG 58.477 50.000 0.00 0.00 0.00 3.66
2691 5362 2.270352 TTTTTGCGGGTGATCTCTGT 57.730 45.000 0.00 0.00 0.00 3.41
2825 5499 8.502105 TCGTCTAGACATCTACATAAACTTCA 57.498 34.615 22.37 0.00 0.00 3.02
2872 5546 7.361457 TCAAAATCAGTTATCCTCGATAGGT 57.639 36.000 0.00 0.00 44.09 3.08
2887 5561 6.872020 ACAAGATGCCTTCATTTCAAAATCAG 59.128 34.615 0.00 0.00 31.96 2.90
2900 5574 7.203255 ACAAAAGTAAGTACAAGATGCCTTC 57.797 36.000 0.00 0.00 0.00 3.46
2905 5579 8.120465 ACAACGAACAAAAGTAAGTACAAGATG 58.880 33.333 0.00 0.00 0.00 2.90
2918 5592 7.274686 AGACAATTAACCAACAACGAACAAAAG 59.725 33.333 0.00 0.00 0.00 2.27
2947 5621 3.704061 ACTGCAAAACAAAGGGCTTCTTA 59.296 39.130 0.00 0.00 34.78 2.10
2995 5669 2.972713 AGGAAGAGGCTTGACAAGTGTA 59.027 45.455 16.39 0.00 0.00 2.90
3130 5804 5.407407 ACAGAACAACGAATAGGATCAGT 57.593 39.130 0.00 0.00 0.00 3.41
3164 5842 8.090788 AGTTTATTCACTAGGAGGAAATGCTA 57.909 34.615 0.00 0.00 0.00 3.49
3255 5945 6.469410 AGTCGGTTTTATTCTTGGTACATGA 58.531 36.000 0.00 0.00 40.83 3.07
3258 5948 8.851541 ATTTAGTCGGTTTTATTCTTGGTACA 57.148 30.769 0.00 0.00 0.00 2.90
3304 5999 2.736978 GGATCAGCTATCAGTGACACG 58.263 52.381 0.00 0.00 36.20 4.49
3306 6001 2.379005 ACGGATCAGCTATCAGTGACA 58.621 47.619 0.00 0.00 40.89 3.58
3314 6009 7.671302 AGATTAACACAATACGGATCAGCTAT 58.329 34.615 0.00 0.00 0.00 2.97
3324 6019 9.594038 GGCACATATTTAGATTAACACAATACG 57.406 33.333 0.00 0.00 0.00 3.06
3330 6025 7.805071 GCATCTGGCACATATTTAGATTAACAC 59.195 37.037 0.00 0.00 43.97 3.32
3382 6081 5.409214 GGGCACGTTACATAAGTGAACTAAA 59.591 40.000 0.00 0.00 38.06 1.85
3383 6082 4.931002 GGGCACGTTACATAAGTGAACTAA 59.069 41.667 0.00 0.00 38.06 2.24
3427 6126 6.642131 TCAAAGCAGAAATAAGCAATTGTGTC 59.358 34.615 7.40 0.00 33.97 3.67
3546 6245 0.889186 ACTTGTTCCATGGCACGTCC 60.889 55.000 6.96 0.00 0.00 4.79
3580 6279 7.067496 TCTGAATCATAAATAGGTCCTCCAC 57.933 40.000 0.00 0.00 35.89 4.02
3591 6290 6.486657 CCACACCCGTATTCTGAATCATAAAT 59.513 38.462 6.10 0.00 0.00 1.40
3629 6328 6.995686 TCTTGTAAAGCATAAACAAGTCCTGA 59.004 34.615 16.04 1.01 46.49 3.86
3650 6349 0.600255 GACAGACCACACCCGTCTTG 60.600 60.000 0.00 0.00 38.54 3.02
3654 6353 1.640917 ATTAGACAGACCACACCCGT 58.359 50.000 0.00 0.00 0.00 5.28
3726 6425 5.405331 AACGACTTTTCTGAGTACAAAGC 57.595 39.130 0.00 0.00 0.00 3.51
3733 6432 5.106830 ACGAAAACAAACGACTTTTCTGAGT 60.107 36.000 0.00 0.00 35.21 3.41
3741 6440 8.913656 TCAAATTTAAACGAAAACAAACGACTT 58.086 25.926 0.00 0.00 0.00 3.01
3742 6441 8.450385 TCAAATTTAAACGAAAACAAACGACT 57.550 26.923 0.00 0.00 0.00 4.18
3767 6466 6.421801 GCACATGCACTGACTTTTTATCTTTT 59.578 34.615 0.00 0.00 41.59 2.27
3771 6470 4.168760 GGCACATGCACTGACTTTTTATC 58.831 43.478 6.15 0.00 44.36 1.75
3772 6471 3.056607 GGGCACATGCACTGACTTTTTAT 60.057 43.478 6.15 0.00 42.27 1.40
3773 6472 2.295909 GGGCACATGCACTGACTTTTTA 59.704 45.455 6.15 0.00 42.27 1.52
3774 6473 1.069049 GGGCACATGCACTGACTTTTT 59.931 47.619 6.15 0.00 42.27 1.94
3781 6480 0.038892 GAACTTGGGCACATGCACTG 60.039 55.000 7.77 3.11 46.62 3.66
3786 6485 2.142356 TATGGGAACTTGGGCACATG 57.858 50.000 0.00 0.00 0.00 3.21
3787 6486 3.403228 AATATGGGAACTTGGGCACAT 57.597 42.857 0.00 0.00 0.00 3.21
3797 6496 7.492344 CCATAAGCTGTTTCAAAATATGGGAAC 59.508 37.037 7.22 0.00 36.33 3.62
3809 6508 2.224992 TGAAGGGCCATAAGCTGTTTCA 60.225 45.455 6.18 0.00 43.05 2.69
3810 6509 2.446435 TGAAGGGCCATAAGCTGTTTC 58.554 47.619 6.18 0.00 43.05 2.78
3811 6510 2.603075 TGAAGGGCCATAAGCTGTTT 57.397 45.000 6.18 0.00 43.05 2.83
3814 6513 1.684983 CCAATGAAGGGCCATAAGCTG 59.315 52.381 6.18 0.00 43.05 4.24
3817 6517 3.569491 ACATCCAATGAAGGGCCATAAG 58.431 45.455 6.18 0.00 0.00 1.73
3824 6524 4.751060 CAAACATGACATCCAATGAAGGG 58.249 43.478 0.00 0.00 0.00 3.95
3853 6553 4.024556 GTGTAGCTAAGCGTAACGAGGATA 60.025 45.833 0.00 0.00 0.00 2.59
3863 6563 3.543680 ATGATTGGTGTAGCTAAGCGT 57.456 42.857 0.00 0.00 0.00 5.07
4068 6768 6.992715 GCTTTCTGCCATAGGAAGAGTTATAA 59.007 38.462 0.00 0.00 43.66 0.98
4156 6856 1.069668 GCATGCAGAAATCAATCCCCC 59.930 52.381 14.21 0.00 0.00 5.40
4297 6999 1.552792 GGCAGAGGAGAGCAAACTACT 59.447 52.381 0.00 0.00 33.23 2.57
4300 7002 1.063183 AAGGCAGAGGAGAGCAAACT 58.937 50.000 0.00 0.00 0.00 2.66
4301 7003 1.163554 CAAGGCAGAGGAGAGCAAAC 58.836 55.000 0.00 0.00 0.00 2.93
4356 7065 1.671054 CAAGTCGGTCGCCAATGGT 60.671 57.895 0.00 0.00 0.00 3.55
4479 7188 2.552802 GCACTTGCTCATGTCTGCT 58.447 52.632 0.00 0.00 38.21 4.24
4562 7271 9.769677 ATATGCAAACCTATACCTAGTCTATGA 57.230 33.333 0.00 0.00 0.00 2.15
4695 7404 5.897377 TCTCAATCGGATATAGCATCGAA 57.103 39.130 0.00 0.00 35.25 3.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.